Hi Ping, Ping Ma wrote: > Dear Dr. Pages, > > I am learning the GenomicRanges in bioconductor. I followed your > notes to do some excise. > My question is whether I can use makeTranscriptDbFromUCSC > > to get relevant gene annonation of */Sulfolobus solfataricus P2/* > http://archaea.ucsc.edu/cgi-bin/hgGateway?db=sulSol1 Unfortunately this is not supported at the moment. The makeTranscriptDbFromUCSC() function is defined in the GenomicFeatures package. I just added the 'url' and 'goldenPath_url' arguments to it, so, *in theory*, the user now should be able to specify the location of an alternate browser. The default values for these arguments are: url="http://genome.ucsc.edu/cgi-bin/" goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath" so, by default, makeTranscriptDbFromUCSC() is using the browser at Santa Clara. To use another browser (e.g. one of the mirror listed on http://genome.ucsc.edu/mirror.html), one would need to do something like: > makeTranscriptDbFromUCSC(genome="sacCer2", tablename="ensGene", url="http://genome.hmgc.mcw.edu/cgi-bin/") Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie The problem is that I get this error with all the browser mirrors I tried. I don't know if it's an issue with the configuration of the remote browser, or with the rtracklayer::browserSession() function that is used behind the scene by makeTranscriptDbFromUCSC() to connect to the remote Genome Browser: > library(rtracklayer) > session <- browserSession(url="http://genome.hmgc.mcw.edu/cgi- bin/") Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie I'm cc'ing Michael Lawrence, the author and maintainer of rtracklayer. Cheers, H. > > Thank you very much. > > Best, > > Ping > > > -- > Ping Ma > Assistant Professor, Department of Statistics > Faculty Member, Institute for Genomic Biology > University of Illinois at Urbana-Champaign -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Dear Dr. Pages. Thank you very much for your quick reply. Ping 2010/6/18 Hervé Pagès <hpages@fhcrc.org> > Hi Ping, > > > Ping Ma wrote: > >> Dear Dr. Pages, >> >> I am learning the GenomicRanges in bioconductor. I followed your notes >> to do some excise. >> My question is whether I can use makeTranscriptDbFromUCSC >> >> to get relevant gene annonation of */Sulfolobus solfataricus P2/* >> http://archaea.ucsc.edu/cgi-bin/hgGateway?db=sulSol1 >> > > Unfortunately this is not supported at the moment. > > The makeTranscriptDbFromUCSC() function is defined in the > GenomicFeatures package. I just added the 'url' and 'goldenPath_url' > arguments to it, so, *in theory*, the user now should be able to > specify the location of an alternate browser. > > The default values for these arguments are: > url="http://genome.ucsc.edu/cgi-bin/" > goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath" > so, by default, makeTranscriptDbFromUCSC() is using the browser > at Santa Clara. > > To use another browser (e.g. one of the mirror listed on > http://genome.ucsc.edu/mirror.html), one would need to do > something like: > > > makeTranscriptDbFromUCSC(genome="sacCer2", > tablename="ensGene", > url="http://genome.hmgc.mcw.edu/cgi-bin/") > Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie > > The problem is that I get this error with all the browser mirrors > I tried. I don't know if it's an issue with the configuration of > the remote browser, or with the rtracklayer::browserSession() > function that is used behind the scene by makeTranscriptDbFromUCSC() > to connect to the remote Genome Browser: > > > library(rtracklayer) > > session <- browserSession(url="http://genome.hmgc.mcw.edu/cgi- bin/") > Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie > > I'm cc'ing Michael Lawrence, the author and maintainer of rtracklayer. > > Cheers, > H. > > > >> Thank you very much. >> >> Best, >> >> Ping >> >> >> -- >> Ping Ma >> Assistant Professor, Department of Statistics >> Faculty Member, Institute for Genomic Biology University of Illinois at >> Urbana-Champaign >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- Ping Ma Assistant Professor, Department of Statistics Faculty Member, Institute for Genomic Biology University of Illinois at Urbana-Champaign [[alternative HTML version deleted]]